def download_xml(pdb_id, dest_dir, silent = True, filename = None, unzip = False):
assert(os.path.exists(dest_dir))
lower_case_gz_filename = os.path.join(dest_dir, '{0}.sifts.xml.gz'.format(pdb_id.lower()))
upper_case_gz_filename = os.path.join(dest_dir, '{0}.sifts.xml.gz'.format(pdb_id.upper()))
lower_case_filename = os.path.join(dest_dir, '{0}.sifts.xml'.format(pdb_id.lower()))
upper_case_filename = os.path.join(dest_dir, '{0}.sifts.xml'.format(pdb_id.upper()))
if filename:
requested_filename = os.path.join(dest_dir, filename)
if os.path.exists(requested_filename):
return read_file(requested_filename)
if unzip == True:
if os.path.exists(lower_case_filename):
contents = read_file(lower_case_filename)
elif os.path.exists(upper_case_filename):
contents = read_file(upper_case_filename)
elif os.path.exists(lower_case_gz_filename):
contents = read_gzip_in_memory(read_file(lower_case_gz_filename))
elif os.path.exists(upper_case_gz_filename):
contents = read_gzip_in_memory(read_file(upper_case_gz_filename))
else:
contents = retrieve_xml(pdb_id, silent = silent, unzip = True)
write_file(os.path.join(dest_dir, filename or '{0}.sifts.xml'.format(pdb_id)), contents)
return contents
else:
if os.path.exists(lower_case_gz_filename):
contents = read_file(lower_case_gz_filename) # Note: read_file already unzips .gz files
if os.path.exists(upper_case_gz_filename):
contents = read_file(upper_case_gz_filename) # Note: read_file already unzips .gz files
else:
gzip_contents = retrieve_xml(pdb_id, silent = silent, unzip = False)
write_file(os.path.join(dest_dir, filename or '{0}.sifts.xml.gz'.format(pdb_id)), gzip_contents)
contents = read_gzip_in_memory(gzip_contents)
return contents
def retrieve_xml(pdb_id, silent = True, unzip = True):
if unzip:
return read_gzip_in_memory(retrieve_file_from_EBI("/pub/databases/msd/sifts/xml/%s.xml.gz" % pdb_id.lower(), silent))
else:
return retrieve_file_from_EBI("/pub/databases/msd/sifts/xml/%s.xml.gz" % pdb_id.lower(), silent)
